Re the Y axis going in the wrong direction - have you uploaded different firmware? The Y axis direction can be reversed in firmware, which may have happened in your case.

The stepsticks need to have vref set before they can be used. They don't come from the factory with the correct setting.

What's happening when you try to start a print from the SD card? Are you able to select a file on the SD card in pronterface (I'm assuming you're kicking it off using pronterface - not sure if you've got the rotary encoder / lcd menu installation)? If so, you at least know the SD card's enabled in the firmware.